Vanilla as in keeping the same guidelines. For example, compare Ubuntu's GNOME with openSUSE's GNOME. Ubuntu doesn't scream "GNOME!", while openSUSE sonar clearly remembers it.
That what I consider here being vanilla, keeping the same style.
Of course every distro always adds its branding and customization, but some look way more similar to the upstream GNOME than others, so... "vanilla GNOME" :)